[gmx-users] Atomtype P,SI not found from grompp
quyviolet at gmail.com
Thu Jan 15 19:58:30 CET 2015
Thanks again! I have downloaded the topology from Automated Topology
Builder (http://compbio.chemistry.uq.edu.au/atb/index.py) using the
Checking all of the *.itp file with both GROMOS 54A7 and GROMOS 534A6
force field for all of the NADPH they provided, I see all of these have the
I would like to ask for your advice in this case.
On Thu, Jan 15, 2015 at 7:37 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> On 1/15/15 1:31 PM, Jennifer Vo wrote:
>> Dear Justin,
>> Thanks a lot, now I got it. I thought P and SI is the two separated atoms
>> so I searched for them two times. Now the
>> grep "P,SI" *.*
>> nap_allatom.itp: 3 P,SI 1 NAP P2B 1 2.247 30.9738
>> nap_allatom.itp: 21 P,SI 1 NAP PA 4 2.315 30.9738
>> nap_allatom.itp: 26 P,SI 1 NAP PN 5 2.259 30.9738
>> should I change "P,SI" to P only?
> If the atom name is an indicator of what the atom is, then presumably
> yes. But I would be wary of any topology in general that used nonsense
> atom types in the parameters it produces, unless there is some additional
> (external) set of parameters upon which this molecule relies, e.g.
> something that defines new parameters and interactions for something called
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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